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Detailed information for vg1207069483:

Variant ID: vg1207069483 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7069483
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.05, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GAATGCAGAGGGAGAAACCGCATTTGATATTGCCAAGAATACCGTTAGCTTCTTCTTCATGGTACGTGATTGACTCCTGCTTCTTCGCTTTTCTTTGGGT[C/A]
GGGGTATCAAGGGTGATTTTATATATGGAACTTTTTAGGGTGCTCCAGACTTTTTTCAAGTCCATCCATTGCCCTCTAATCCATTAATGGATGATATTCC

Reverse complement sequence

GGAATATCATCCATTAATGGATTAGAGGGCAATGGATGGACTTGAAAAAAGTCTGGAGCACCCTAAAAAGTTCCATATATAAAATCACCCTTGATACCCC[G/T]
ACCCAAAGAAAAGCGAAGAAGCAGGAGTCAATCACGTACCATGAAGAAGAAGCTAACGGTATTCTTGGCAATATCAAATGCGGTTTCTCCCTCTGCATTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.00%	23.00%	0.63%	23.32%	NA
All Indica	2759	61.60%	36.60%	0.33%	1.49%	NA
All Japonica	1512	33.30%	3.20%	0.99%	62.50%	NA
Aus	269	67.70%	5.20%	0.00%	27.14%	NA
Indica I	595	18.50%	80.30%	0.34%	0.84%	NA
Indica II	465	80.90%	17.40%	0.22%	1.51%	NA
Indica III	913	78.00%	20.90%	0.11%	0.99%	NA
Indica Intermediate	786	63.70%	33.10%	0.64%	2.54%	NA
Temperate Japonica	767	34.70%	5.50%	0.65%	59.19%	NA
Tropical Japonica	504	21.00%	0.80%	0.60%	77.58%	NA
Japonica Intermediate	241	54.80%	0.80%	2.90%	41.49%	NA
VI/Aromatic	96	79.20%	3.10%	0.00%	17.71%	NA
Intermediate	90	50.00%	14.40%	6.67%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207069483	C -> DEL	N	N	silent_mutation	Average:45.007; most accessible tissue: Callus, score: 69.081	N	N	N	N
vg1207069483	C -> A	LOC_Os12g12820.1	downstream_gene_variant ; 2116.0bp to feature; MODIFIER	silent_mutation	Average:45.007; most accessible tissue: Callus, score: 69.081	N	N	N	N
vg1207069483	C -> A	LOC_Os12g12810.1	intron_variant ; MODIFIER	silent_mutation	Average:45.007; most accessible tissue: Callus, score: 69.081	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207069483	NA	1.31E-07	mr1170	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	8.50E-08	mr1268	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	1.35E-06	mr1272	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	3.93E-06	mr1531	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	1.16E-06	mr1549	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	2.97E-06	mr1673	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207069483	NA	7.94E-06	mr1750	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251